In the Shadow of Time
by Dazrika
Summary: A dark power has risen in Hyrule, on the heel of Ganon's defeat, the world has begun to rebuild. But a dark reflection has risen and made itself solid, beginning to gather fragments of dark power. (Next part up. Was longer, cut about half of it off because part of it seemed like it should take more time. Comments/Criticism/Hate Mail, send it. T for some possible violence later on )
1. Chapter 1

The Deku Tree and the Kokiri had long had a connection with the abandoned manor at the center of the Lost Woods. Built on sacred ground, it was dubbed a temple shortly after the deaths of its original occupants. One of the early forest sages had created the pedestal that sat in front, bearing the image of the forest medallion, at about the same time the other sages created similar pedestals outside the other time wore on, the temple was slowly reclaimed by the forest, both inside and out. But with one small step, Ganon had made a grab for one of the keys to the Sacred Realm, ensured the death of the Great Deku Tree, and the corruption of the forest and the temple. The Lost Woods had always been a mysterious and dangerous place, but with the loss of the Great Deku Tree and the spread of Ganon's darkness, the woods had twisted even further.

The woods surrounding the temple had been corrupted more than the areas surrounding any temple, and was likely only exceeded by the corruption of the land surrounding where Ganon's Castle once stood. This dark influence had twisted the normal creatures of the forest, and invited more to make the area their home, making it dangerous to even approach the temple to attempt to purify it entirely. Even after three years, despite the best efforts of the Kokiri, the Sages, the Deku Tree Sapling, the Kokiri Woods and Village had barely been restored to their former glory, leaving both the Temple and Lost Woods infested.

Saria stared sadly into the maze, remembering all the days she had spent sitting on the stump in front of the Forest Temple, playing her Ocarina in the warm sun…. Now, she would likely get run through with a spear before she could even hope to reach her old spot. Even with the powers that had awakened, she wasn't much of a fighter. She missed being able to walk through the old manor like she once had… but while getting to her old spot was difficult, entering the temple was now impossible. When she and the other sages had determined that the Temple would be extremely difficult to purify, even as a group, she and the Deku Sapling had erected a powerful barrier at the entrance. Better to keep the evil that was already there in, and keep more evil from getting in.

She was snapped out of her thoughts by a voice calling to her from behind her. She turned around and tilted her head, looking into the dark void to the Lost Woods, trying to pinpoint the source of the voice. "Mido?" she called, a note of confusion in her voice. Something was wrong, there was a note of panic in the shout. She began to call to him again, when a cold shiver ran through her body, and the words were lost. A cloud of dark mist passed through her, moving in the direction of the maze. Her whole body shook as she watched one of the moblins approach the mist. She let out a gasp as the faintest shape of a sword formed in the mist, and cut the creature down with ease. "It… it can't be… that's not…" she stuttered, as she took a few involuntary steps forward.

She stumbled forward a little more, before breaking into a run. She rounded the first corner of the maze just in time to see another Moblin cut down in the same way, the mist beginning to move faster down the correct path to reach the Forest Temple. Saria moved to break into another run, before being stopped by something pulling on her hand. The pounding in her ears, which she hadn't noticed until now, began to calm enough to hear Mido calling her name again, this time much closer. She turned to see him holding her hand, breathing heavily and hunched over.

"M-Mido? What's wrong?"

He released Saria's hand, but he took a moment to catch his breath before he responded. "R… ran… from Great… Deku Tree…." He paused again, taking a moment to calm himself down a little more. "The Great Deku Tree said something evil was coming ta the forest, and we saw that thing take the shortcut through the Woods straight through to the village, and then straight ta the Lost Woods. I… I was worried about you," he said, looking away and his face turning slightly red at the last part.

Saria looked toward her old clearing, and then back to Mido. "Does the Great Deku Tree know what it is?"

Mido shook his head, clutching a slingshot in his hand. The fairy slingshot… Zelda had given the sages Link's old things, and she had given Mido back the Kokiri Sword and the Fairy Slingshot. "No, but we know where it's going," he said with a grunt, swallowing as the death shout of the Moblin Brute rose from the grove. Both started moving carefully toward the Forest Temple, before they were forced to stop to clutch their ears, a piercing whistle echoing through the entire Lost Woods. After a moment of listening, Saria's eyes grew wide as she heard a familiar tune in the noise. She once again took off running, catching Mido by surprise before he could take off running after her. "Saria! Wait!"

Saria froze as she reached the top of the stairs, staring into her secret place. The mist was just floating at the side of the clearing, not moving or doing anything, but this wasn't why she froze. The grove was different than the last time she had seen it, but the same. It was mirroring the calm it had been three years ago, looking exactly as it had when she had gone to try and clear the Temple herself. It was a patch of peace surrounded by chaos. In the center of the clearing, there stood two phantoms of the path; Link and Sheik. The two were as ghosts, she was able to see through them to the temple beyond, but she heard the sound as Sheik lifted her harp, and Link his Ocarina, and they began to perform the Minuet of the Forest. She was rooted to the spot, fixated on the scene in front of her, either unable to, or unwilling to, wrap her mind around what was going on in front of her. Mido soon joined her, just as dumbstruck.

As the song ended, Sheik faded away, and Link looked around, looking like he was trying to figure out where she had vanished to. After a moment he pulled his hookshot from his belt and shot himself up to the balcony, and entered the temple. After he… it… whatever, entered, the illusion began to fade, the overgrown and dangerous present taking the place of the serene past. The severed 'heads' of several Deku Baba were scattered around the clearing, and vines and weeds covered the Forest Medallion Pedestal. The mist began to move again, floating up to the top of the destroyed staircase and attempted to enter the temple, only to find its way barred by the barrier.

Saria managed to snap herself out of her trance, starting to call on her powers as the Forest Sage. She was hoping she could use some of the barrier's power to consume the mist.

Mido put a deku nut in his slingshot and pulled it back, hoping that it might do something to its target. He fired, but it simply passed through and bounced off the barrier. Saria's power was too slow to respond, and both were helpless as the form of a sword appeared in the mist once more, and sliced through the barrier like it wasn't there. As it split open, there was an explosion of magical backlash. It left the mist unharmed, but the two Kokiri were thrown down the stairs by the force.

Saria was able to use the magic she was building to absorb most of the impact, and another cold shiver went down her spine as she felt the mist enter the temple, her temple. She struggled to get back up to her feet, and rushed to check on Mido. He hadn't been as lucky as her, and appeared to have been knocked unconscious by the force of the blast. Other than a little battered, he appeared to be fine though. She breathed a sigh of relief and moved him down to flat ground to lay. "I'll be back," she whispered gently, before rushing after the mist.

The monsters that inhabited the entryway to the temple were on the ground, very dead. She knew that they would be back, or more would take their place though. If it were that easy to cleanse the temple of their darkness, Nabooru or Darunia would have cleared the temple out. However, the force with which the creatures had been slain terrified her. From the fact that the Mido's deku nut had just passed right through the mist, it didn't appear that the creatures could've harmed the mist at all. Whatever it was, it was just killing them for the sake of killing them. She followed the path of death and destruction to the center room, making it just in time to see the last of the mist float down through the elevator.

She ran to the center, leaping down the stairs and onto the elevator. She was very worried now. Up until now she could pretend that there was something else that was in the temple that the mist could have been after, but there was only one thing in the basement. She could only pray to the goddesses that she wasn't right.

She made it down and ran up the stairs to the gallery, the door appearing to have been blown apart. She ignored it, but was suddenly overcome by a wave of evil energy as she entered the room. It took every ounce of willpower she had to not collapse. She slowly made her way up the spiral staircase, seeing the mist move in a tornado around the center of the room, forming a column between the high ceiling and the single spot. "I… I'm too late," was all she managed to muster out, her horror quite close to sealing off her voice completely, as she watched a portal open up on the floor beneath the column.

From the portal rose a figure… His figure. The mist began to latch itself onto the phantom, restoring its form. She tried to force her horror away, trying to muster her power to force both the phantom and the mist back into the portal. However, the phantom raised its hand, and she was forced to lunge of the way of a ball of black energy it shot at her. She could only watch as the mist restored the Phantom to its old form and power. True, it was only a fraction of His original power, but if He had escaped in some spirit form or something and was trying to get a body….

But her train of thought and theories were shattered as she watched the phantom begin to change shape. It had dark skin, a black tunic, and glowing red eyes, but everything else… everything else was his. "L… Link? Is… is that you? How is this possible?"

The figure did nothing to acknowledge her before opening a pouch on its belt and throwing a deku nut at her, vanishing in a burst of white light, leaving her shivering, confused and alone on the ground.


	2. Chapter 2

"Watch your form, Princess! That might work with your little knife, but Gerudo blades are made of tougher stuff!" Nabooru goaded, easily dodging a clumsy swing from the twin blades. Princess Zelda, her opponent, was not necessarily the target of her taunting. She gave a playful glance over at Impa, who was watching the pair off to the side, along with several of the Gerudo guards.

Princess Zelda had made it her goal to help all the races recover from the aftereffects of Ganon's dark influence, personally. She was also using it as an opportunity to further the training she had started under Impa, and learn more about Hyrule. While she had been Sheik, she had not had as much freedom to travel and explore, especially the Gerudo sands. She had entered the lion's den on one or two occasions, but she had been careful to give Koume and Kotake a wide berth. The pair might have been able to sense the magic that was protecting her from Ganon's gaze, or something worse.

The land where both her and Ganon's castles once stood had been badly disturbed by his darkness, and she was reluctant to build there again. She had decided to have the castle be rebuilt away from the city, that way if someone attempted to attack again, her people would not be in as much danger. Hyrule Castle Town had been purged of the darkness that resided within, and the town had taken steps to begin rebuilding. Many were, understandably, reluctant to return to the village, and chose to remain and Kakariko. Still, others had returned to their old homes and business, helping to rebuild the once thriving city to its former glory.

From there, she had spent much time in the Kokiri woods, working with Saria and the Deku tree to purge the darkness that had corrupted the woods. The area around the Forest Temple had been un-salvageable, but, with a lot of time and patience, they had managed to remove the influence from the village and some of the surrounding woods. Both the Deku Tree and Kokiri had assured her that, with time, the woods would fully return to normal. The Gorons had refused her help, claiming that they had not suffered much from their time. He had only just managed to overwhelm them when Link had awoken and rescued them from being fed to Volvagia. The Zora King and Princess Ruto gave much the same answer, that, with time, Zora's Domain would return to normal.

So, the Princess had set out for the Gerudo sands, spending time training with Nabooru. She was determined not to force their entire race to suffer for the crimes of their leader, and Nabooru was determined to stamp out anyone who remained loyal to Ganon and his designs. Still, progress with helping the Gerudo recover had been... slow. It had been the seat of power for Ganon and his minions for so long, some were doubtful they would even be able to purge his taint from their lands. Not to mention, many of the Gerudo, despite feeling that they were at fault for what happened, were uncomfortable accepting the princess' help. Even Nabooru, who had been fairly welcoming, refused to let her aide in some things.

"I think that's enough daydreaming!" Nabooru called, moving forward quickly, and prepared to deliver a one-two punch to the princess. Zelda did her best to try and block the blow, but she needn't have bothered. It didn't actually come, as Nabooru fell to her knees and started clutching her head. "Stop... stop... stop your damn laughing!" she shouted, a look of panic on her face.

Zelda dropped her blades and moved over to her, several of the watching Gerudo doing the same. As she approached, Zelda froze as well, feeling a dark energy as she approached. She looked around wildly, trying to figure out where exactly it was coming from. As she turned, she saw Impa doing the same, albeit in a much more calculated manner, and with a hand on her own blade. But, just as soon as the energy had come, it was quickly starting to fade. She could not pinpoint where it was coming from... it was as if a dark energy had spread across all of Hyrule in a moment, and then completely vanished again. "Are you alright, Nabooru?" Zelda asked, approaching the fallen sage, who appeared to be coming to her senses once again.

"I'm fine," she grunted, ignoring several hands attempting to help her up and getting up on her own. "I just felt... darkness, and... magic? Their magic..." She trailed off, her tone suggesting she was talking more to herself than anyone present. She shook her head slightly, looking at Zelda as if she hadn't seen her there. "I think that's enough practice with me for the day. You can use the training grounds, if you want. I need to... go." With a slight bow, she moved across the rooftop, down into the fortress. The princess could barely make out her speaking to one of the guards that followed her. "Wake Aveil. She needs to go to the Colossus."

The Princess turned back to Impa, who was still scanning the area around them. From the top of the fortress they could see for miles in the desert, but they could not see anything that could have caused the disturbance. Her guardian took her hand off her blade, but didn't appear to have relaxed much. "Are you okay, Impa?"

She looked back, thinking carefully before she spoke. "I am fine, Princess. But, I feel as if I have felt that energy before. It is not quite the energy that Ganondorf gave off, but I can feel it. The essence of the Shadow Temple lies within it." She turned to face her charge, looking over the Gerudo who were still standing there carefully, seemingly deep in thought. "I am going to need to leave you here, temporarily, princess."

The princess took a step back, slightly taken aback by the suddenness. After a moment, however, she regained her composure and nodded to Impa, understanding why she had to go. The Shadow Temple, more than all the others, was a seat of evil. Meant to imprison the darkness of Hyrule's past, the dark power within it needed to be protected from evil seeking to steal that power. "You have my leave, secure your temple."

"Remain here, I will return shortly." She jumped off the top of the fortress, rolling as she landed, before moving swiftly toward the canyon.

Zelda watched her for as long as she could, crossing her arms and sighing. She had hoped that this was over, she had hoped that there would be peace for a time. But it seemed that Hyrule had been robbed of even the smallest respite. They had been so close... so close...


End file.
